Infection with intestinal nematodes induces profound pathological changes to the gut that are associated with eventual parasite expulsion. We have applied expression profiling as an initial screening process with oligonucleotide microarrays (Affymetrix MG-U74AV2 gene chips) and time course kinetics to investigate gene transcription triggered by the intraepithelial nematode Trichinella spiralis in jejunal epithelium from BALB/c mice. Of the 4,114 genes detected, 2,617 were present in all uninfected and T. spiralis-infected replicates, 8% of which were notably upregulated, whereas 12% were downregulated at the time of worm expulsion (day 14 postinfection). Upregulation of goblet cell mucin gene transcripts intestinal mucin gene 3 (MUC3), calcium chloride channel 5 (CLCA5), and goblet cell gene 4 (GOB4) is consistent with enhanced production and alteration of mucus, whereas a 60-to 70-fold upregulation of transcripts for mast cell proteases 1 and 2 (MCPT-1 and -2) is consistent with intraepithelial mucosal mast cell recruitment. Intestinal infection can induce substantial pathological changes in the epithelial compartment (1, 37, 59). These may be preceded by specific immune responses in the lamina propria, Peyer's patches and mesenteric lymph nodes (66) and may trigger the activation of intraepithelial lymphocytes and the recruitment of inflammatory cells into the epithelial compartment (7, 39). The epithelium can itself respond to pathogens, for example, by the secretion of chloride ions and water by enterocytes (11, 51), by increased polyimmunoglobulin receptor-mediated transport of pathogen-specific immunoglobulin A (IgA) across the enterocytes (10), and by the release of mucus from goblet cells and of antimicrobial peptides from Paneth cells (37, 49). Thus, the resulting elimination of the pathogen and the associated pathology will be a complex product of both innate and pathogen-specific effector mechanisms.The intestinal nematode Trichinella spiralis dwells within epithelium and actively invades epithelial cells (36,69). This is associated with major pathological changes within the epithelial compartment such as villus atrophy and crypt hyperplasia, increased epithelial permeability, goblet cell and Paneth cell hyperplasia, and infiltration by mucosal mast cells (20,25). Some of these profound changes are immunologically mediated and are temporally associated with the rejection of adult worms (25, 33). Infection of BALB/c mice with T. spiralis is a particularly well-characterized model of infection, where parasite expulsion is partially dependent on the recruitment and activity of mucosal mast cells (28,65) Although the molecular pathology of intestinal infection is generally studied in the context of specific mechanisms, a global approach such as that afforded by transcriptomics may highlight some of the molecular pathways involved or indeed bring novel mechanisms to light. The aim of the present study was to examine, by using oligonucleotide microarrays (Affymetrix MG-U74AV2), the effect of T. spiralis on ...